Stromal Clusters

Gene Expression

Endothelial cells

Lymphatic Endothelial cells

Enteric Glia cells

Vascular Smooth Muscle cells (VSMCs)

Pericytes

Fibroblasts

Myofibroblasts

CAFs

Clusters’ Gene Markers

Cluster 0

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
ADAMDEC1 3.68733172068316 0.995 0.17 0
CCL13 3.5388141656568 0.64 0.077 0
CCL8 3.06666462677878 0.7 0.081 0
APOE 2.65946863586292 0.977 0.373 0
CTSC 2.36640495931904 0.957 0.437 0
HAPLN1 2.18465468658638 0.739 0.075 0
STMN2 2.16071557188795 0.68 0.086 0
ADAM28 1.96356266277764 0.674 0.073 0
ABCA8 1.94385324578853 0.813 0.224 0
TCF21 1.8062301073721 0.861 0.348 0
CCL2 1.76723353816083 0.882 0.4 0
CCL11 1.75728469862459 0.54 0.163 0
LINC01082 1.67779584496377 0.74 0.187 0
EDIL3 1.6187840917385 0.641 0.197 0
RBP1 1.57196643333244 0.831 0.351 0
MFAP4 1.52252727913899 0.94 0.508 0
PPAP2B 1.47795189118892 0.38 0.085 0
APOC1 1.47553292167395 0.525 0.15 0
CYGB 1.45675367222024 0.759 0.294 0
CXCL14 1.45378954611166 0.971 0.323 0

Cluster 1

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
COMP 3.12122165892103 0.472 0.033 0
MMP11 2.96916995709418 0.625 0.127 0
COL1A1 2.96463402164057 0.964 0.636 0
CTHRC1 2.96383473246103 0.816 0.24 0
FN1 2.4545893705844 0.829 0.498 0
COL1A2 2.3644502008234 0.975 0.718 0
CST1 2.30011085206192 0.178 0.016 0
COL3A1 2.2559841065282 0.977 0.67 0
SULF1 2.24626077915287 0.771 0.186 0
THBS2 2.2181439564839 0.777 0.201 0
COL10A1 2.1903722597173 0.624 0.022 0
SFRP4 2.16864292650039 0.523 0.11 0
INHBA 2.13515346237315 0.731 0.103 0
BGN 2.13229774242432 0.829 0.405 0
POSTN 2.09216954769972 0.885 0.277 0
COL12A1 1.99639800544459 0.775 0.266 0
COL11A1 1.97765385266778 0.613 0.022 0
COL5A1 1.97319969459855 0.853 0.321 0
AEBP1 1.96745880469827 0.868 0.476 0
COL5A2 1.91192593706939 0.821 0.344 0

Cluster 2

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
C7 3.52311811669677 0.726 0.088 0
DPT 3.12905857783409 0.811 0.241 0
THBS4 2.43826360163228 0.359 0.031 0
CCL11 2.29438667511532 0.615 0.171 0
LY6H 2.17875232988057 0.236 0.01 0
ADH1B 2.04832945490018 0.854 0.27 0
KCNN3 2.02138313109817 0.443 0.076 0
MGP 1.99110899305373 0.822 0.606 0
GSN 1.89654427209342 0.985 0.828 0
OGN 1.83341869692197 0.66 0.172 0
SRPX 1.79585034827864 0.673 0.275 0
APOD 1.61988854865332 0.498 0.185 0
CCDC80 1.5240206902937 0.816 0.435 0
CXCL12 1.47932315322554 0.866 0.473 0
PID1 1.45584700532227 0.497 0.136 0
DCN 1.44267694993538 0.989 0.617 0
FBLN1 1.44125197215109 0.942 0.53 0
C1QTNF3 1.34031177087711 0.485 0.17 0
RAMP1 1.80136244836497 0.368 0.131 2.93219856136628e-270
SMOC2 1.35246041960593 0.377 0.135 1.63097091279239e-257

Cluster 3

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
MFAP5 2.68995281802333 0.659 0.148 0
IGFBP6 2.67855390893076 0.885 0.531 0
CFD 2.37140148021627 0.995 0.435 0
TNXB 2.28521557389545 0.767 0.246 0
PLAC9 2.12551357295466 0.911 0.438 0
PCOLCE2 2.02389550067404 0.569 0.077 0
FBN1 1.87145654000628 0.654 0.36 0
SFRP1 1.80456084159034 0.582 0.163 0
SLPI 1.75445321712692 0.349 0.09 0
EFEMP1 1.73191969433416 0.777 0.366 0
DCN 1.67612313533767 0.995 0.619 0
CCDC80 1.65326548768179 0.777 0.441 0
S100A4 1.51872203416247 0.948 0.702 0
GSN 1.49429793927267 0.987 0.829 0
ADH1B 1.48690648008088 0.803 0.278 0
PI16 1.48159646012688 0.469 0.073 0
SFRP2 1.44464136103636 0.576 0.243 1.00578628349672e-273
SERPINE2 1.46510616150215 0.609 0.298 5.61947316796055e-273
CD55 1.70159063415458 0.6 0.352 8.02273550200621e-241
PLA2G2A 2.08055216583982 0.293 0.082 8.45688407081346e-233

Cluster 4

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
F3 3.02998670660047 0.816 0.204 0
DMKN 2.83210863762376 0.717 0.162 0
CXCL14 2.77476231438307 0.957 0.359 0
FRZB 2.75081724736162 0.811 0.2 0
HSD17B2 2.73642764414378 0.721 0.041 0
NSG1 2.666450101953 0.717 0.051 0
VSTM2A 2.5863657238234 0.606 0.017 0
PLAT 2.54306060456282 0.904 0.467 0
POSTN 2.44479665312084 0.839 0.304 0
ENHO 2.35141795546664 0.628 0.029 0
BMP4 2.20877066509439 0.783 0.282 0
EDNRB 2.07599681418097 0.688 0.171 0
GADD45G 1.83554179184186 0.528 0.188 0
PDGFRA 1.82538716647587 0.631 0.314 0
AGT 1.82383322298387 0.47 0.076 0
CXCR4 1.7851303248266 0.47 0.129 0
RGS10 1.76699190692144 0.723 0.353 0
FENDRR 1.75519520122659 0.561 0.137 0
BMP5 1.74677997645638 0.514 0.067 0
SOX6 1.74428762729774 0.452 0.051 0

Cluster 5

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
ACKR1 4.06180796183931 0.746 0.024 0
DARC 3.04727697273501 0.144 0.001 0
VWF 2.61911717218711 0.904 0.133 0
CLDN5 2.51678095364416 0.795 0.127 0
CD74 2.46945838389021 0.962 0.475 0
SELE 2.31278727842361 0.38 0.016 0
AQP1 2.28050242733378 0.628 0.102 0
HLA-DRA 2.26725809331332 0.875 0.281 0
HLA-DRB1 2.24000009927288 0.872 0.257 0
RAMP3 2.20134651802251 0.847 0.114 0
DUSP23 2.081772534482 0.777 0.229 0
RNASE1 1.97120373756767 0.848 0.179 0
PECAM1 1.93064749096327 0.773 0.128 0
TSPAN7 1.89685381945227 0.667 0.089 0
HLA-DPA1 1.78438773721144 0.768 0.294 0
HLA-DPB1 1.69222410640321 0.759 0.296 0
EDN1 1.69049142021186 0.343 0.045 0
ARL4A 1.6828825745766 0.693 0.187 0
MADCAM1 1.6588079167039 0.261 0.009 0
NPDC1 1.65470167654465 0.848 0.323 0

Cluster 6

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
HSPG2 2.73525364944289 0.926 0.388 0
COL4A1 2.66987502023081 0.921 0.409 0
ESM1 2.54036087128448 0.365 0.008 0
INSR 2.41179330891198 0.758 0.149 0
PLVAP 2.38932501597573 0.924 0.138 0
VWF 2.32902161070062 0.87 0.138 0
CD93 2.30998778951513 0.835 0.108 0
COL15A1 2.26343277999764 0.846 0.293 0
PECAM1 2.24889688546242 0.854 0.125 0
PODXL 2.24335202728401 0.77 0.089 0
FLT1 2.15287632650436 0.731 0.092 0
COL4A2 2.13052433133426 0.877 0.455 0
RGCC 2.10824269218263 0.8 0.218 0
VWA1 2.07099436366007 0.825 0.157 0
RAMP2 1.97737257511345 0.901 0.258 0
ENG 1.97728314287229 0.89 0.39 0
FKBP1A 1.908196210364 0.959 0.701 0
EGFL7 1.88338780696219 0.864 0.165 0
PCDH17 1.86955704964928 0.67 0.068 0
ADGRL4 1.86902964540824 0.761 0.1 0

Cluster 7

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
CD320 4.03701701382091 0.881 0.243 0
PLVAP 3.94963962927034 0.927 0.14 0
FABP5 3.66591089835893 0.969 0.371 0
CA4 3.51673686412478 0.431 0.021 0
CD36 3.17630344475657 0.781 0.051 0
RGCC 2.95204803878484 0.71 0.225 0
CD74 2.84477570567519 0.968 0.477 0
SRGN 2.83234657690063 0.938 0.235 0
CLDN5 2.78961993765805 0.837 0.128 0
TMEM88 2.62588719073136 0.808 0.072 0
HLA-DRB1 2.57395119367535 0.921 0.258 0
ENPP2 2.54900224743347 0.598 0.103 0
SLC9A3R2 2.5279551823791 0.862 0.315 0
SDPR 2.51514130433821 0.833 0.165 0
RAMP2 2.43485241542636 0.954 0.257 0
RBP7 2.42561117277619 0.617 0.046 0
HLA-DRA 2.3049421013489 0.861 0.285 0
GNG11 2.25805466649229 0.972 0.613 0
FLT1 2.22386453761039 0.727 0.093 0
IFI27 2.21347508812685 0.993 0.678 0

Cluster 8

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
RGS5 4.42033614106272 0.909 0.07 0
NDUFA4L2 3.04663391111955 0.877 0.141 0
NOTCH3 2.38548555476468 0.844 0.121 0
COL4A1 2.29285583861126 0.886 0.412 0
HIGD1B 2.1843510932232 0.578 0.015 0
ACTA2 2.17281621149233 0.877 0.401 0
COX4I2 2.10619355197618 0.593 0.023 0
PDGFRB 2.09841152672157 0.831 0.266 0
LINC00152 2.07977209231326 0.808 0.367 0
COL18A1 2.07150200636072 0.88 0.464 0
MIR4435-2HG 1.94379733917385 0.702 0.252 0
COL4A2 1.88165434735665 0.867 0.456 0
STEAP4 1.71576467705183 0.38 0.032 0
GJA4 1.71274638259961 0.589 0.057 0
ITGA1 1.69848240091131 0.734 0.249 0
CALD1 1.66488931071842 0.99 0.873 0
LHFP 1.65281247774031 0.832 0.412 0
RGS16 1.65169503307457 0.6 0.184 0
MCAM 1.63011511878748 0.722 0.174 0
TINAGL1 1.55882993958595 0.637 0.166 0

Cluster 9

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
S100B 4.97625495817153 0.959 0.01 0
CRYAB 4.81293569079028 0.981 0.343 0
GPM6B 4.74856265224753 0.957 0.052 0
PLP1 4.18859063532468 0.895 0.007 0
LGI4 3.9105419268264 0.86 0.054 0
ALDH1A1 3.75402436493581 0.882 0.24 0
NRXN1 3.66631382007125 0.798 0.002 0
SPP1 3.59785196471453 0.681 0.087 0
CLU 3.48511278049771 0.973 0.326 0
CD9 3.27430501845725 0.986 0.611 0
FXYD1 3.26728872990635 0.87 0.339 0
CDH19 3.22872423844963 0.713 0.002 0
SEMA3B 3.0266759781971 0.766 0.106 0
MYOT 2.93694099083187 0.65 0.002 0
MPZ 2.84730995856502 0.583 0.009 0
PRNP 2.8263488187616 0.855 0.429 0
MAL 2.79971131697004 0.627 0.003 0
SCN7A 2.78233725417074 0.619 0.053 0
PMP22 2.7383287359406 0.969 0.621 0
TPPP3 2.71625194584385 0.593 0.272 1.14743434098402e-289

Cluster 10

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
MMP3 3.99922024332052 0.3 0.028 0
MMP1 3.92541314348451 0.425 0.075 0
CXCL1 3.02435955943379 0.584 0.164 0
CHI3L1 2.45723502682882 0.385 0.043 0
IL24 1.86068722519521 0.172 0.005 0
CXCL6 1.79406228388889 0.32 0.038 0
CXCL5 1.79343621286028 0.277 0.009 0
F3 1.52468915445285 0.672 0.219 0
AGT 1.46233576079336 0.413 0.084 0
PDPN 1.40482963140826 0.669 0.222 0
SOD2 2.05252189968551 0.749 0.414 2.7396054819007e-301
CXCL8 3.66008301965318 0.413 0.112 6.15465964984643e-301
CXCL3 1.64692716883461 0.396 0.101 1.11882612962445e-290
FTH1 1.52486363605018 1 0.992 1.62347105395858e-187
CXCL14 1.51828998832191 0.699 0.381 4.2526565457902e-187
IER3 1.6842925833943 0.634 0.373 1.75209501620592e-151
AREG 1.84773117109545 0.188 0.049 2.81743916516366e-117
IL6 1.55152055306384 0.232 0.071 2.51315957115448e-115
G0S2 1.51718046141373 0.379 0.2 3.81127467632324e-72
IGJ 1.86382455131508 0.233 0.192 4.95016989802096e-05

Cluster 11

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
PTGDS 3.0263837775063 0.811 0.262 0
C3 2.15671804352781 0.718 0.257 0
IGF1 1.67122193595444 0.562 0.147 0
FBLN1 1.15313160175112 0.961 0.541 0
CCL19 3.26631520699634 0.191 0.023 1.97902970224716e-285
COL14A1 1.17879401001901 0.748 0.333 9.69408415148516e-276
SERPINF1 1.21573054731822 0.911 0.55 2.02666906556883e-272
CCDC80 1.6228282642334 0.793 0.448 3.9273588769309e-263
SFRP2 2.00842711750134 0.598 0.249 1.41693479526891e-255
RARRES1 1.71076087386875 0.445 0.14 4.59759002846626e-251
SFRP4 2.26472766727855 0.435 0.137 5.47703509630294e-234
CCL11 1.76556514794873 0.527 0.189 6.29835978533223e-228
PLA2G2A 2.30831684162477 0.329 0.085 7.85276505976695e-226
APOD 2.33842527668764 0.49 0.195 2.71020706308026e-176
MGP 1.6569095006402 0.75 0.616 1.20468888775962e-127
SERPINE2 1.17800176569201 0.543 0.308 2.28598023134134e-81
CCL21 1.38762265704013 0.141 0.047 4.69774903121774e-53
IGLC3 1.33353734169363 0.502 0.358 2.72024590900523e-33
IGJ 2.01947472359195 0.288 0.189 6.14797363692281e-27
JCHAIN 1.37457327208527 0.249 0.38 1.35040252871662e-26

Cluster 12

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
MFAP5 3.40796366636005 0.977 0.15 0
SFRP2 3.25188335200962 0.948 0.237 0
MGP 2.96914404033152 0.998 0.607 0
PCOLCE2 2.81972284048101 0.959 0.076 0
CFD 2.80441831574691 1 0.452 0
WISP2 2.78691380981358 0.942 0.082 0
IGFBP6 2.71915323831523 0.995 0.537 0
DCN 2.69079416996497 1 0.631 0
PI16 2.5849976406046 0.922 0.066 0
DPT 2.43478484597215 0.979 0.256 0
EFEMP1 2.38560383810323 0.994 0.369 0
MGST1 2.31511276868589 0.968 0.167 0
SLPI 2.29530991097704 0.728 0.081 0
GPNMB 2.21193877790971 0.978 0.276 0
CES1 2.19099360301446 0.871 0.095 0
OGN 2.18221031288281 0.975 0.177 0
PLAC9 2.15255948551525 0.994 0.45 0
ADH1B 2.13432197569829 0.997 0.286 0
OSR2 2.11365403688843 0.884 0.076 0
CD55 2.0211839810853 0.937 0.345 0

Cluster 13

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
RERGL 3.79350704091076 0.796 0.005 0
MYH11 3.76201157779014 0.948 0.076 0
ADIRF 3.72945165633803 0.992 0.539 0
PLN 3.44595784227306 0.853 0.069 0
TAGLN 3.27349698276081 0.992 0.403 0
ACTA2 3.10242675667355 0.972 0.406 0
MYL9 2.86166502390406 0.988 0.677 0
DSTN 2.7802588173192 0.986 0.796 0
SNCG 2.51468759748464 0.713 0.144 0
MT1M 2.51370784737228 0.709 0.129 0
CSRP2 2.46374746567767 0.804 0.182 0
TPM2 2.39224116104506 0.975 0.589 0
MT1E 2.31089754931177 0.798 0.344 0
SORBS2 2.23018098331674 0.748 0.144 0
C2orf40 2.22851261993086 0.533 0.037 0
CRIP1 2.19591466885023 0.77 0.273 0
BCAM 2.08128692430013 0.78 0.188 0
NET1 2.03011616434287 0.684 0.125 0
FLNA 2.00992774667792 0.897 0.484 0
MT1X 2.52768271789138 0.72 0.314 5.31432800425957e-297

Cluster 14

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
SERPINE1 2.83603650968143 0.753 0.152 0
COL1A1 2.66812627748393 0.979 0.661 0
COL3A1 2.56482258121048 0.994 0.693 0
IGF1 2.49727133514613 0.761 0.151 0
SGK1 2.14844452065614 0.679 0.179 0
CRABP2 1.84370192591705 0.689 0.138 0
GAS1 1.71023964943042 0.643 0.143 0
MMP23B 1.56003008365853 0.786 0.225 0
ERRFI1 1.6599372778331 0.701 0.214 7.31206105499206e-300
ABL2 1.41237501184814 0.732 0.225 1.17428616299345e-299
TNFRSF12A 1.39539504318831 0.721 0.221 5.07929909587332e-289
COL1A2 2.23524000690673 0.978 0.737 2.69730284609063e-286
COL5A1 1.49530790779691 0.842 0.361 7.05063368886224e-267
C3 1.76532253012614 0.755 0.266 8.64950589436685e-267
CTHRC1 1.6950802501442 0.762 0.285 1.15686888381742e-254
KRT8 1.42776674553964 0.737 0.294 2.15050548483256e-221
SPARC 1.6582419233652 0.952 0.858 1.543180090797e-209
CYR61 1.99504872968872 0.803 0.507 8.72407959261943e-177
BGN 1.46944961514368 0.784 0.439 1.2522628115425e-165
KLF6 1.58975945329063 0.793 0.549 2.22079035523973e-161

Cluster 15

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
RPL31 1.0360970508438 0.99 0.95 1.42266103767063e-155
RP11-400N13.3 1.12255656209113 0.241 0.041 5.03414773426729e-139
ZFAS1 1.12294115179002 0.707 0.634 2.90337020048823e-52
GAPDH 1.2372940284299 0.955 0.931 9.52981743952504e-51
MIF 1.18555492557957 0.641 0.564 3.09027987037476e-43
SPINK1 1.28970487765804 0.148 0.04 3.99036740103499e-43
TIMP1 1.53571019623204 0.917 0.875 2.34854878855874e-33
ALDOA 1.04443078581995 0.732 0.759 8.00882912757509e-32
BNIP3 1.05409581549067 0.325 0.228 2.79744219523949e-14
ENO1 1.33357478215108 0.584 0.64 1.48881947068041e-13
APOD 1.44668983215005 0.08 0.213 8.66673039333961e-11
FN1 1.36694254450008 0.565 0.531 9.29890185375327e-08
MT2A 1.42980417777467 0.587 0.633 0.000700042920503399
ANGPTL4 1.01382225258329 0.219 0.168 0.0408843386456483

Cluster 16

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
ACTG2 5.24214981669115 0.953 0.087 0
DES 4.80700372023202 0.58 0.054 0
SOSTDC1 3.52592725638905 0.335 0.008 0
MYH11 3.51374276032651 0.901 0.091 0
CNN1 3.40673150502723 0.789 0.128 0
TAGLN 3.34449716811464 0.995 0.413 0
MYLK 3.31358996030505 0.931 0.27 0
MYL9 3.03980971777013 0.998 0.682 0
TPM2 2.93998444890468 0.992 0.595 0
ACTA2 2.81445492895384 0.978 0.415 0
PCP4 2.21817157451794 0.242 0.003 0
HHIP 2.1916010168002 0.374 0.038 0
PLN 2.11358768676793 0.561 0.088 0
CKB 2.81407718719544 0.693 0.191 6.41521594628673e-301
TPM1 2.36529134785158 0.98 0.656 2.56292578736228e-273
SYNPO2 1.91205104297677 0.574 0.126 5.68558713979495e-265
PDLIM3 2.07731694111924 0.802 0.301 1.0410444220529e-249
CSRP1 2.40965784547905 0.855 0.422 1.28681827402172e-246
SMTN 2.6177579144678 0.736 0.264 3.18728968424241e-246
FLNA 2.3133878753225 0.893 0.491 2.70550508163193e-231

Cluster 17

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
SRGN 2.97695163037587 0.974 0.263 0
CLDN5 2.78089583889422 0.953 0.156 0
RAMP2 2.51613206085392 0.979 0.285 0
ICAM2 2.47968311753889 0.898 0.17 0
CLEC14A 2.3662513831663 0.921 0.175 0
PECAM1 2.24697818245181 0.847 0.157 0
GJA5 2.11301866288464 0.616 0.014 0
PODXL 2.11197349722357 0.767 0.119 0
HEY1 2.03487388417536 0.712 0.076 0
PTPRB 2.01102322402649 0.812 0.108 0
GIMAP4 1.99682731403015 0.781 0.127 0
TM4SF1 2.41234949331346 0.998 0.481 2.91003711480976e-239
SLC9A3R2 2.47082883654206 0.923 0.336 1.91237414523848e-230
C10orf10 2.38965762969883 0.816 0.225 5.17671448617941e-229
KCTD12 2.29359546613729 0.786 0.231 6.1034991499032e-227
EPAS1 2.08626308223211 0.914 0.356 6.47376649221107e-227
SRP14 2.23549313530998 1 0.91 7.87199294610907e-223
IFI27 2.20885442953197 0.993 0.691 1.19366907193112e-212
CAV1 2.10334841899405 0.97 0.541 5.45427748095218e-171
IGFBP3 2.32739909732284 0.76 0.291 6.00692472598139e-136

Cluster 18

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
CCL21 7.21463425681987 0.949 0.04 0
TFF3 4.96263862712249 0.964 0.25 0
MMRN1 3.66946237801817 0.854 0.017 0
LYVE1 3.58841097940466 0.803 0.018 0
SDPR 2.82518724174138 0.91 0.192 0
CLDN5 2.71679695368511 0.908 0.158 0
ECSCR.1 2.647267498916 0.875 0.135 0
PROX1 2.42483772223138 0.708 0.01 0
LAPTM5 2.18861613114108 0.696 0.072 0
NTS 2.11784143960237 0.228 0.001 0
ARL4A 2.20350159323901 0.816 0.21 1.04559578654492e-247
TFPI 3.07280744863644 0.962 0.441 8.60920689195125e-244
PPFIBP1 2.20426955409642 0.826 0.294 1.21677421113837e-196
PTPRE 1.70377091748411 0.678 0.156 4.82439598755351e-195
MGST2 1.8610040684022 0.785 0.253 6.2530633014407e-179
SNCG 1.7042433786812 0.655 0.158 9.52411849531322e-168
GNG11 2.16419647990483 0.936 0.629 2.7332463943393e-155
AKAP12 2.20047864192244 0.79 0.323 1.24780816901389e-144
ARL6IP1 1.72851340920566 0.859 0.41 9.11594866162524e-137
FABP4 2.00038990772647 0.529 0.158 8.23107249778758e-93

Cluster 19

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
LTB 2.83032443916233 0.656 0.033 0
CD52 2.71941034531196 0.864 0.057 0
CD3D 2.65787257757715 0.888 0.033 0
KLRB1 2.47541765371216 0.552 0.02 0
TRBC2 2.21107669751475 0.736 0.027 0
CD2 2.12455396629469 0.808 0.014 0
CD7 2.01497463372937 0.688 0.025 0
CORO1A 1.99169822799141 0.848 0.044 0
TRBC1 1.98071042644058 0.48 0.016 0
CD3E 1.93963030993518 0.776 0.013 0
PTPRC 1.818439171646 0.736 0.019 0
NKG7 1.83731635985815 0.344 0.018 6.58633429869938e-154
CD69 2.23327676531049 0.656 0.067 9.20199150938871e-151
RGS1 2.77711022336831 0.76 0.1 2.78970277435948e-143
CCL5 2.75749458298394 0.52 0.046 6.48154962337873e-141
TRAC 2.28291433075129 0.848 0.139 9.52668057013872e-127
CXCR4 2.55623384912081 0.824 0.148 1.8592053915736e-106
GZMB 1.89716848912333 0.272 0.018 5.27454609784267e-95
SRGN 1.95888579806675 0.992 0.271 1.0218418887393e-84
CCL4 2.02399531670009 0.328 0.072 1.094486036595e-26

Cluster 20

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
HP 3.9588460781162 0.672 0.002 0
UPK3B 3.33774065973915 0.672 0.004 0
MSLN 2.26071909092946 0.714 0.025 0
PRG4 2.13088931751935 0.521 0.004 0
HAS1 2.04463726594409 0.84 0.04 0
SERPINB2 2.03122379678635 0.311 0.004 0
CLDN1 1.94110133258107 0.824 0.017 0
EGFL6 2.01795756457758 0.655 0.045 3.30068319843696e-217
ITLN1 4.745639869128 0.387 0.018 9.06714906830672e-190
SLPI 4.73743177153731 0.807 0.106 2.55172080023463e-147
KRT19 3.52462004067397 0.933 0.164 3.00667315940159e-141
PLA2G2A 3.07308429768732 0.731 0.095 2.71631726557572e-128
RARRES1 2.2846660752009 0.849 0.153 1.09092879465849e-109
C3 3.47007160026359 0.983 0.277 8.8756755883292e-108
KRT8 2.43238680126009 1 0.304 5.02648086054151e-92
KRT18 2.62673474015371 0.908 0.257 3.25595685700309e-78
PTGDS 2.26493228817745 0.966 0.286 4.636696544282e-72
MT1E 2.18649678928017 0.983 0.358 7.44220097508192e-71
MT2A 2.140021676262 1 0.63 2.4942158069253e-51
IL6 1.98473027167364 0.395 0.078 5.6744077317068e-35

Cluster 21

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
KIAA0101 2.64066938603775 0.973 0.034 0
TYMS 2.28943169436318 0.959 0.043 0
UBE2C 2.22889025426432 0.811 0.022 0
RRM2 2.04557595447697 0.865 0.011 0
TK1 1.90127716167846 0.932 0.036 0
PTTG1 1.91088371115842 0.797 0.063 1.91589515336651e-149
APLNR 1.75709765498763 0.892 0.1 1.81153310366749e-107
CD93 2.01394303374681 1 0.147 3.38149809498726e-93
PECAM1 1.85082094404409 1 0.165 4.28374212252291e-75
STMN1 2.30213655700521 1 0.273 7.93309244982217e-62
VWF 1.83621316958339 0.932 0.178 1.84040058139078e-58
COL15A1 2.18653208478799 1 0.323 1.4215728381108e-50
H2AFZ 2.45020079101636 1 0.64 1.82827658649388e-44
HMGB2 1.9162710799906 0.946 0.314 2.37251363853343e-44
COL4A1 2.39307966195376 0.973 0.437 3.18255257708994e-40
HSPG2 1.80450088891959 0.973 0.417 9.22898324474528e-35
FKBP1A 1.81454743949009 1 0.715 9.7177141060873e-35
COL4A2 1.8927458216245 0.973 0.477 1.6352688596345e-33
TUBA1B 1.9573409688163 1 0.758 2.63593134783911e-32
HIST1H4C 2.44671879905272 0.838 0.334 4.69016433067122e-23

First annotations

Clusters Annotation Clusters Annotation
0 Fibroblasts 11 Fibroblasts
1 Fibroblasts (CAFs?) 12 Fibroblasts
2 Fibroblasts 13 VSMCs?
3 Fibroblasts 14 Fibroblasts (CAFs?)
4 Fibroblasts? 15 Fibroblasts
5 Vascular Endothelial cells 16 Myofibroblasts?
6 Vascular Endothelial cells 17 Vascular Endothelial cells
7 Vascular Endothelial cells 18 Lymphatic Endothelial cells
8 Pericytes? 19 Fibroblasts
9 Enteric glia 20 Fibroblasts
10 Fibroblasts 21 Vascular Endothelial cells

Hierarchical Clustering of Stromal Clusters

Fibroblasts vs CAFs

Clusters 1 and 14 seem to be cancer associated fibroblasts (CAFs). Thus, cells in each of these two clusters will be separated into ‘normal’ and ‘tumour’ based on source sample and expression markers analysed again, as well hierarchical clustering. This separation is done because cells from normal samples grouped in clusters assigned as CAFs should not be classified as CAFs.

Merge some clusters together and find new markers

Considering previous results, the following clusters were merged together:

Following merge, markers were calculated for the new clusters:

Cluster 5_6_7_17_21

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
PLVAP 4.46954445021959 0.862 0.025 0
CLDN5 3.50621816037353 0.756 0.031 0
VWF 3.4467987224475 0.85 0.024 0
CD320 3.30152750158031 0.683 0.184 0
RAMP2 3.18388777398319 0.921 0.15 0
PECAM1 3.0210800470765 0.77 0.027 0
CD74 2.92155106585902 0.839 0.426 0
FABP5 2.90175117320177 0.762 0.32 0
ACKR1 2.87942506484282 0.306 0.012 0
RAMP3 2.855041896541 0.755 0.019 0
RNASE1 2.82434945143106 0.849 0.073 0
SRGN 2.80392594919161 0.829 0.145 0
EGFL7 2.61991092330747 0.832 0.06 0
RGCC 2.55021827308036 0.576 0.176 0
HLA-DRB1 2.54600914793142 0.769 0.184 0
AQP1 2.50847496031399 0.536 0.04 0
CLEC14A 2.46251610282164 0.79 0.045 0
CD93 2.43169388872286 0.718 0.018 0
HSPG2 2.42684276822925 0.802 0.33 0
CA4 2.33373293833249 0.149 0.019 0

Cluster 1Tumor_14Tumor

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
COL1A1 3.72414108849909 0.997 0.631 0
CTHRC1 3.35252207072076 0.98 0.219 0
COMP 3.23168705168313 0.561 0.021 0
COL1A2 2.91715904780823 0.998 0.714 0
COL3A1 2.88646788282248 0.996 0.667 0
MMP11 2.82532835578986 0.599 0.128 0
THBS2 2.51556020899984 0.948 0.178 0
FN1 2.50453557536009 0.974 0.48 0
BGN 2.49611839948268 0.987 0.385 0
SFRP4 2.33578489148556 0.645 0.094 0
INHBA 2.26004805939474 0.829 0.089 0
CST1 2.25634147259074 0.175 0.015 0
SULF1 2.23140216368791 0.857 0.174 0
COL5A1 2.20730494769233 0.95 0.307 0
COL5A2 2.17407293468095 0.958 0.326 0
COL10A1 2.15265562130255 0.616 0.02 0
COL12A1 2.0896965922481 0.908 0.249 0
AEBP1 2.07547376323788 0.971 0.462 0
SPARC 2.01390555778222 0.996 0.845 0
COL11A1 1.95531044191962 0.606 0.02 0

Cluster 1Normal_14Normal_0_2_3_4_10_11_12_15_19_20

Gene Average Log2FC % Expressed in cluster % Expressed others p-value adjusted
CFD 5.54893224906756 0.778 0.137 0
ADAMDEC1 4.82293279857468 0.442 0.068 0
CXCL14 3.9254281109547 0.628 0.139 0
APOE 3.64748282458714 0.593 0.274 0
CCL13 3.50777359640726 0.252 0.018 0
DPT 3.28754471296295 0.457 0.095 0
CCL11 3.27222363979871 0.35 0.045 0
DCN 3.13375078472838 0.893 0.372 0
ADH1B 2.97369765279194 0.579 0.023 0
MFAP4 2.82359011670778 0.831 0.253 0
CCL8 2.81271854804316 0.261 0.031 0
FBLN1 2.61772263751093 0.824 0.27 0
IGFBP6 2.33157445381628 0.69 0.407 0
TCF21 2.19104482901169 0.644 0.141 0
PTGDS 2.18498913312685 0.392 0.174 0
MT-RNR2 2.08348499241654 0.351 0.099 0
CTSC 1.977620140192 0.593 0.39 0
MT-RNR1 1.9648386039357 0.34 0.091 0
MFAP5 2.24574630731684 0.253 0.109 1.41564179997817e-284
MGP 2.08297832428887 0.524 0.733 0.00133886143979436

Second annotations

Clusters Annotation Clusters Annotation
5_6_7_17_21 Vascular Endothelial Cells 13 VSCMs
18 Lymphatic Endothelial Cells 16 Myofibroblasts
9 Enteric Glia 1Normal_14Normal_0_2_3_4_10_11_12_15_19_20 Fibroblasts
8 Pericytes 1Tumor_14Tumor CAFs